Smith is a better shot blocker and a much better stealer over their careers. I know there is more to defense then that, but Smith is much more versatile defender able to guard every PF and a lot of centers and SF's (especially in short bursts). Bogut is not a great help defender and can't even effectively guard half the centers in the league because he lacks the lateral quickness. He does fine against guys like Bynum, Kaman, Camby, Perkins, etc. but really struggles against the quicker guys like Horford, Howard, Chandler, etc.
Head to head against Bogut:Horford averages 12 & 7
Chandler averages 10 & 10
Howard averages 17 & 13 (to be fair, Howard owns Bogut on the other end of the floor)
While historically Smith is the better shotblocker between the two; Smith's numbers continue to decrease while Bogut's increase.
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Smith is unquestionably more versatile, but if you give me the option of a versatile 3/4 or a strong defensive center I'm taking the latter every time.